https://github.com/taha-parsayan/xml-metadata-extractor

Extracting metadata related to MRI and PET images from xml files
https://github.com/taha-parsayan/xml-metadata-extractor

brain metadata metadata-extraction mri pet xml xmlfile

Last synced: 30 days ago
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Extracting metadata related to MRI and PET images from xml files

• Host: GitHub
• URL: https://github.com/taha-parsayan/xml-metadata-extractor
• Owner: taha-parsayan
• License: apache-2.0
• Created: 2024-08-19T12:21:52.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-08-19T12:44:15.000Z (4 months ago)
• Last Synced: 2024-08-20T22:45:12.223Z (4 months ago)
• Topics: brain, metadata, metadata-extraction, mri, pet, xml, xmlfile
• Language: Python
• Homepage:
• Size: 32.2 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# XML metadata extractor

### Description

Typically, MRI and PET images contain metadata within xml files. Each subject has it's own xml file and therefore, it would be time-consumming to open all the files one by one and read their information to report in an article.

In here, I provided 2 python files to automatiically open and read the xml files for MRI and PET metadata within the related folders.

### Extracted information for MRI:

Manufacturer: The name of the manufacturer of the imaging equipment.

Pixel Spacing X: The pixel spacing in the X direction.

Pixel Spacing Y: The pixel spacing in the Y direction.

Slice Thickness: The thickness of the imaging slices.

Matrix X: The number of pixels in the X dimension of the image matrix.

Matrix Y: The number of pixels in the Y dimension of the image matrix.

Matrix Z: The number of pixels in the Z dimension of the image matrix.

Mfg Model: The model of the imaging equipment.

Pulse Sequence: The pulse sequence used in the imaging.

TE (Echo Time): The echo time parameter used in the imaging.

TR (Repetition Time): The repetition time parameter used in the imaging.

Coil: The type of coil used in the imaging.

Image Resolution: A string combining Matrix X, Matrix Y, Matrix Z, Pixel Spacing X, Pixel Spacing Y, and Slice Thickness into a descriptive format.

### Extracted information for PET:

Manufacturer: The name of the manufacturer of the imaging equipment.

Image Resolution:

Number of Rows: Number of rows in the image matrix.

Number of Columns: Number of columns in the image matrix.

Number of Slices: Number of slices in the image stack.

Pixel Spacing X: The pixel spacing in the X direction.

Pixel Spacing Y: The pixel spacing in the Y direction.

Slice Thickness: Thickness of each image slice.

Image Resolution Format: Combines the number of rows, columns, slices, pixel spacings, and slice thickness into a single descriptive string.

Mfg Model: The model of the imaging equipment.

Reconstruction: The type of reconstruction used in the imaging process.

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### How to use

Put all the MRI and PET xml files in two separate folders. There are two codes provided in here, one for MRI and one for PET.

within the codes, set the address of the folders in:

Define the directory where your XML files are located

directory = 'E:\SDU_University\PhD Project\Paper - KAN\Metadata\METADATA-PET-ALL'

Run the code. The 'pd' variable contains the information in a dataframe.

Enjoy.

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You are free to:

- Share — copy and redistribute the material in any medium or format

- Adapt — remix, transform, and build upon the material

- for any purpose, even commercially.

Under the following terms:

- Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.